Here are my musings on the 40k Apocalypse :
The Emperor is dying and the throne failing. One of the high lords of Terra (inquisitor) hears the Voice (ala Talon of Horus) of the Emperor and this Inquisitor brings Cypher to the throne and end the emperors life. The Emperor dies and a laugh echoes through the chamber and the 5th Chaos god is reborn.
The Emperor's death scream calls forth Vulkan, Corax, Dorn (armless of course), Lion El Jonson, and Guilliman, they return to their legions and break ties with Terra. The Ecclesiarchy views this new god as a continuation of the Emperor, and they as well as the Militarum fall to this new god. The Mechanium withdraws to mars and a civil war ensues over if this new god is still the omnihassa (sp?). The inquisitors go to war linked to the side of the "new emperor" chaos god.
Meanwhile in the Warp Abbaddon and the fallen primarchs realize the death of the Emperor and feel the release of a new god. The legions gather and strike at Cadia, overwhelming it easily.
Eldar and Dark Eldar view the "new emperor" as the reincarnation of the old ones and make all haste to Terra.
The Tyranids' hive mind also having sensed the Astronomica failing, move in, similarily the necrons sensing a dire threat completely wake up. The Orks being orks just love that there is a fight going on and start a strong invasion.
The old loyalist legions again are split between their primarchs return and loyalty to Terra. Blood angels sensing the danger, scour their legions and finally eliminate their flaw by spilling each other's blood.
We end at a place where the prodigal and lost sons return and team up making a new empire of daemon and man where they are untied against this evil. The new emperor and his legions are seen as the "bad guys" and their cult has killed billions across the galaxy and are the new force now allied with the Eldar but this new god is far darker than any other chaos god and threats to defeat them and enter an age of total oblivion. Orks are still orks, more tyranids everywhere.
This doesn't really account for the death of anyone but we could kill off a number of ways. I just like the way this shakes up the universe, more power players, the return of legions of marines and the "good guys" being bad
I can expand more on my thoughts but I am in class haha